Q:

I am developing a software for assessing similarity among flexible proteins. I
would like to test the software on the Database of Macromolecular Movements
to test my software, however I found no means to download multiple files. I
was wondering whether it is possible to get a data set with files containing
protein motions without separately accessing each and every entry in your
database.

What I would like to have, if it is possible of course, is the curated
files of the conformational changes and the corresponding PDB IDs. Let
me know whether it is possible or not.

A:

This may be doable, but it depends on what exactly you need. Do you want the frame-by-frame morph files, the video files, or the PDB IDs, or some other form of the data? Also, we actually have two databases: one is a manually curated set of about 200 conformational changes, and the other database is user-submitted. If you tell me more about the kinds of things you may need, I can likely send you the compressed files.

At the first URL below, you will find the curated set of motions. The second URL is an outbox that’s prepared for you, which contains these morphs (frame-by-frame) from the curated motions:

http://www.molmovdb.org/cgi-bin/browse.cgi

http://homes.gersteinlab.org/people/dc547/.curated_morphs__G_Mate/

Please let us know if you have trouble getting access for any reason.